Multiple sequence alignment - TraesCS6A01G237100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G237100 chr6A 100.000 3641 0 0 1 3641 446726400 446730040 0.000000e+00 6724
1 TraesCS6A01G237100 chr6D 94.740 3004 123 20 668 3641 309951860 309954858 0.000000e+00 4639
2 TraesCS6A01G237100 chr6D 90.343 642 27 12 1 627 309951238 309951859 0.000000e+00 809
3 TraesCS6A01G237100 chr6B 94.669 2889 122 10 1 2866 477788095 477790974 0.000000e+00 4453
4 TraesCS6A01G237100 chr6B 91.395 430 22 5 3219 3641 477791322 477791743 3.150000e-160 575
5 TraesCS6A01G237100 chr6B 84.709 327 20 14 2863 3167 477791008 477791326 2.130000e-77 300
6 TraesCS6A01G237100 chr5A 84.076 314 50 0 2075 2388 32703181 32703494 1.640000e-78 303
7 TraesCS6A01G237100 chr5A 76.022 367 83 5 1166 1530 32702683 32703046 6.210000e-43 185
8 TraesCS6A01G237100 chr5D 83.439 314 52 0 2075 2388 42922906 42923219 3.560000e-75 292
9 TraesCS6A01G237100 chr5D 75.487 359 86 2 1166 1523 42922393 42922750 1.340000e-39 174
10 TraesCS6A01G237100 chr4A 80.000 315 61 2 2078 2391 598590780 598591093 7.860000e-57 231
11 TraesCS6A01G237100 chr5B 76.567 367 81 5 1166 1530 38168277 38167914 2.870000e-46 196


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G237100 chr6A 446726400 446730040 3640 False 6724 6724 100.000000 1 3641 1 chr6A.!!$F1 3640
1 TraesCS6A01G237100 chr6D 309951238 309954858 3620 False 2724 4639 92.541500 1 3641 2 chr6D.!!$F1 3640
2 TraesCS6A01G237100 chr6B 477788095 477791743 3648 False 1776 4453 90.257667 1 3641 3 chr6B.!!$F1 3640
3 TraesCS6A01G237100 chr5A 32702683 32703494 811 False 244 303 80.049000 1166 2388 2 chr5A.!!$F1 1222
4 TraesCS6A01G237100 chr5D 42922393 42923219 826 False 233 292 79.463000 1166 2388 2 chr5D.!!$F1 1222

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
960 977 0.979187 TGCCCCTAGGAACTAACCCG 60.979 60.000 11.48 0.00 42.17 5.28 F
1281 1298 1.572415 AGGGATGATGCATTGGAACCT 59.428 47.619 0.00 2.81 0.00 3.50 F
1485 1502 1.612442 TGAGGACCTCCCCTTTCCG 60.612 63.158 19.11 0.00 36.49 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2286 0.850100 ATGTTGGGTGAACTGGACCA 59.150 50.000 0.00 0.0 34.89 4.02 R
2296 2421 1.000385 CGAACACCACGGTACCACTTA 60.000 52.381 13.54 0.0 0.00 2.24 R
3233 3422 1.135972 GCATTGTTCGCGTTGTCTGAT 60.136 47.619 5.77 0.0 0.00 2.90 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 232 1.677576 GCATTTGCTCCATTCCGATCA 59.322 47.619 0.00 0.00 38.21 2.92
254 269 2.038557 TCTCTTGGCAGAAACCAGGTAC 59.961 50.000 0.00 0.00 41.82 3.34
350 365 5.838521 ACCCACTTATAATTTAGGGCCATTG 59.161 40.000 6.18 0.00 39.97 2.82
365 380 5.103086 AGGGCCATTGAATTATTTCTAGGGT 60.103 40.000 6.18 0.00 39.63 4.34
472 488 3.066621 TGCTGGTAAGACTTGCAAAACAG 59.933 43.478 8.47 8.47 0.00 3.16
570 586 5.874093 TGGCAAATCCACAACCATAAATTT 58.126 33.333 0.00 0.00 40.72 1.82
638 655 8.884124 ACCATCAAAATTCTGAAGGAATAGAA 57.116 30.769 9.95 0.00 43.17 2.10
639 656 9.312904 ACCATCAAAATTCTGAAGGAATAGAAA 57.687 29.630 9.95 0.00 43.17 2.52
640 657 9.578439 CCATCAAAATTCTGAAGGAATAGAAAC 57.422 33.333 0.00 0.00 43.17 2.78
641 658 9.282247 CATCAAAATTCTGAAGGAATAGAAACG 57.718 33.333 0.00 0.00 43.17 3.60
642 659 8.391075 TCAAAATTCTGAAGGAATAGAAACGT 57.609 30.769 0.00 0.00 43.17 3.99
643 660 8.504005 TCAAAATTCTGAAGGAATAGAAACGTC 58.496 33.333 0.00 0.00 43.17 4.34
680 697 1.737236 GCACACAAGTTCTCACACACA 59.263 47.619 0.00 0.00 0.00 3.72
767 784 4.562757 CCCGGACTTAGAAATGAGTTGACA 60.563 45.833 0.73 0.00 0.00 3.58
920 937 4.518249 CCCTTTTGCTGGGTTTTTGTTTA 58.482 39.130 0.00 0.00 39.82 2.01
929 946 8.367660 TGCTGGGTTTTTGTTTATTATATCCA 57.632 30.769 0.00 0.00 0.00 3.41
960 977 0.979187 TGCCCCTAGGAACTAACCCG 60.979 60.000 11.48 0.00 42.17 5.28
979 996 5.067273 ACCCGTTCACAATTTGATCTAACA 58.933 37.500 2.79 0.00 32.84 2.41
1079 1096 4.301072 AGATTGGTCGGAATCCTTTGAA 57.699 40.909 0.00 0.00 33.46 2.69
1281 1298 1.572415 AGGGATGATGCATTGGAACCT 59.428 47.619 0.00 2.81 0.00 3.50
1290 1307 2.224744 TGCATTGGAACCTGCTGAACTA 60.225 45.455 6.63 0.00 37.00 2.24
1305 1322 6.163476 TGCTGAACTATACGACAATGAGTTT 58.837 36.000 0.00 0.00 30.66 2.66
1383 1400 2.210116 GTGGACAACGACAATGTGACT 58.790 47.619 0.00 0.00 0.00 3.41
1416 1433 3.136443 AGTCACCACACCAGATTGAGAAA 59.864 43.478 0.00 0.00 0.00 2.52
1448 1465 2.034221 GGCACTGAAGGGGGTGAC 59.966 66.667 0.00 0.00 35.69 3.67
1485 1502 1.612442 TGAGGACCTCCCCTTTCCG 60.612 63.158 19.11 0.00 36.49 4.30
1512 1529 3.055819 ACACATTTGACCGCTATGTCTCT 60.056 43.478 0.00 0.00 36.21 3.10
1615 1632 7.010923 CAGCTTGAGTAGGCTAGTATTTTCTTG 59.989 40.741 0.89 0.00 37.00 3.02
1633 1650 2.496899 TGACCTTCATCCTTTCCTGC 57.503 50.000 0.00 0.00 0.00 4.85
1649 1666 6.041069 CCTTTCCTGCTGCTACTTACTACTAT 59.959 42.308 0.00 0.00 0.00 2.12
1713 1731 7.396540 AGATTTGTAGCCAATCCAGTTTTAG 57.603 36.000 0.00 0.00 0.00 1.85
1830 1848 4.970662 TGATAATGCTCTTGTTTCCAGC 57.029 40.909 0.00 0.00 0.00 4.85
1848 1866 3.464907 CAGCTGTCCATGATTCGAGAAT 58.535 45.455 5.25 0.00 0.00 2.40
1930 1954 6.374417 AGACATGTACAGATACCTTTGGTT 57.626 37.500 0.00 0.00 37.09 3.67
1931 1955 7.490657 AGACATGTACAGATACCTTTGGTTA 57.509 36.000 0.00 0.00 37.09 2.85
2161 2286 1.966762 CGGGCTTGCCTGTTTGATT 59.033 52.632 12.07 0.00 0.00 2.57
2182 2307 1.886542 GGTCCAGTTCACCCAACATTC 59.113 52.381 0.00 0.00 37.48 2.67
2296 2421 1.077429 GCTCAAAAGGATCGGGCCT 60.077 57.895 0.84 0.00 40.93 5.19
2453 2578 5.132502 TCTCAATGTTCCAAGTGTGTTGAT 58.867 37.500 0.00 0.00 0.00 2.57
2457 2582 6.714356 TCAATGTTCCAAGTGTGTTGATATCA 59.286 34.615 0.00 0.00 0.00 2.15
2487 2613 1.270550 GGTATGTTGTTGCTGCAGCTT 59.729 47.619 36.61 15.95 42.66 3.74
2683 2809 4.678509 TTTTGGCTTCTGTATGTTAGCG 57.321 40.909 0.00 0.00 34.50 4.26
2733 2859 7.649306 ACTCATGTATGTTTGTGCTTTTCTTTC 59.351 33.333 0.00 0.00 0.00 2.62
2873 3036 5.263599 TGCATCCTCTAACATGGTGAAAAT 58.736 37.500 0.00 0.00 0.00 1.82
2880 3043 5.964758 TCTAACATGGTGAAAATTGCCATC 58.035 37.500 0.00 0.00 40.68 3.51
2960 3128 6.527423 TGTTAGGTTCAAATTCGGTAAGTCT 58.473 36.000 0.00 0.00 0.00 3.24
2974 3142 4.448060 CGGTAAGTCTCCTTGTTGTCTTTC 59.552 45.833 0.00 0.00 31.89 2.62
2999 3167 9.782900 TCATATATCCTGTATTCCTGTATTCCA 57.217 33.333 0.00 0.00 0.00 3.53
3049 3217 2.874701 CACACACTGGAAGAGGAAACAG 59.125 50.000 0.00 0.00 37.43 3.16
3054 3222 2.089980 CTGGAAGAGGAAACAGGCATG 58.910 52.381 0.00 0.00 34.07 4.06
3055 3223 1.704628 TGGAAGAGGAAACAGGCATGA 59.295 47.619 4.84 0.00 0.00 3.07
3056 3224 2.108075 TGGAAGAGGAAACAGGCATGAA 59.892 45.455 4.84 0.00 0.00 2.57
3057 3225 2.751806 GGAAGAGGAAACAGGCATGAAG 59.248 50.000 4.84 0.00 0.00 3.02
3058 3226 3.416156 GAAGAGGAAACAGGCATGAAGT 58.584 45.455 4.84 0.00 0.00 3.01
3059 3227 3.064900 AGAGGAAACAGGCATGAAGTC 57.935 47.619 4.84 0.00 0.00 3.01
3061 3229 0.169009 GGAAACAGGCATGAAGTCGC 59.831 55.000 4.84 0.00 0.00 5.19
3062 3230 1.160137 GAAACAGGCATGAAGTCGCT 58.840 50.000 4.84 0.00 0.00 4.93
3064 3232 1.726853 AACAGGCATGAAGTCGCTAC 58.273 50.000 4.84 0.00 0.00 3.58
3065 3233 0.608130 ACAGGCATGAAGTCGCTACA 59.392 50.000 4.84 0.00 0.00 2.74
3066 3234 1.208052 ACAGGCATGAAGTCGCTACAT 59.792 47.619 4.84 0.00 0.00 2.29
3067 3235 1.863454 CAGGCATGAAGTCGCTACATC 59.137 52.381 0.00 0.00 0.00 3.06
3068 3236 1.482182 AGGCATGAAGTCGCTACATCA 59.518 47.619 0.00 0.00 37.70 3.07
3069 3237 1.863454 GGCATGAAGTCGCTACATCAG 59.137 52.381 0.00 0.00 36.81 2.90
3070 3238 2.481969 GGCATGAAGTCGCTACATCAGA 60.482 50.000 0.00 0.00 36.81 3.27
3106 3295 7.156000 AGAAGAGATCATATGCTCTGAACATG 58.844 38.462 13.65 0.00 40.43 3.21
3173 3362 7.363431 ACATTACAAAAGAAAAGTAGAGCAGC 58.637 34.615 0.00 0.00 0.00 5.25
3185 3374 9.265901 GAAAAGTAGAGCAGCTATATGATTCAA 57.734 33.333 0.00 0.00 0.00 2.69
3205 3394 9.662947 GATTCAACATGTATGATATCATGGAGA 57.337 33.333 25.44 7.98 43.68 3.71
3393 3588 7.765695 ACAGGACACATTTTCAGAACATAAT 57.234 32.000 0.00 0.00 0.00 1.28
3432 3628 0.321653 AACAGATCACCTCCAACGCC 60.322 55.000 0.00 0.00 0.00 5.68
3433 3629 1.296392 CAGATCACCTCCAACGCCA 59.704 57.895 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 0.742281 CATCACAGAAGAGGCACCGG 60.742 60.000 0.00 0.00 0.00 5.28
145 146 0.036952 ACATCACAGAAGAGGCACCG 60.037 55.000 0.00 0.00 0.00 4.94
217 232 3.933861 AGAGACCCAAGAACAACAGTT 57.066 42.857 0.00 0.00 0.00 3.16
254 269 3.529634 TCAACCAAAGTAAATCGTGCG 57.470 42.857 0.00 0.00 0.00 5.34
350 365 7.803131 ACTGGTCCTTACCCTAGAAATAATTC 58.197 38.462 0.00 0.00 46.16 2.17
359 374 7.728981 TCAGATAATTACTGGTCCTTACCCTAG 59.271 40.741 12.27 0.00 46.16 3.02
365 380 7.373617 TGCATCAGATAATTACTGGTCCTTA 57.626 36.000 12.27 0.00 36.22 2.69
527 543 4.397417 GCCACTTCATATCTTGAACTTGCT 59.603 41.667 0.00 0.00 39.44 3.91
570 586 1.283613 GATGTGGACATGGGGGTTGTA 59.716 52.381 0.00 0.00 36.57 2.41
680 697 3.056962 TGTGTGCAAGATTTGTGTGTGTT 60.057 39.130 0.00 0.00 0.00 3.32
767 784 2.091885 TGGAGACAAGTTCTTGGCCTTT 60.092 45.455 13.91 0.00 37.44 3.11
850 867 6.375455 ACAAATCTTTGCGAGTTCTTCCATAT 59.625 34.615 2.63 0.00 41.79 1.78
920 937 6.239402 GGGCAAGAAAATGCTGTGGATATAAT 60.239 38.462 0.00 0.00 45.68 1.28
929 946 2.450476 CTAGGGGCAAGAAAATGCTGT 58.550 47.619 0.00 0.00 45.68 4.40
960 977 7.872163 TGCAATGTTAGATCAAATTGTGAAC 57.128 32.000 0.00 0.00 40.50 3.18
979 996 6.238953 GCCATTTCTTGATCTCTGTATGCAAT 60.239 38.462 0.00 0.00 0.00 3.56
1079 1096 1.107945 CCGGACACCACCTTTGTTTT 58.892 50.000 0.00 0.00 0.00 2.43
1281 1298 5.324784 ACTCATTGTCGTATAGTTCAGCA 57.675 39.130 0.00 0.00 0.00 4.41
1290 1307 7.442969 TCAACAACCTTAAACTCATTGTCGTAT 59.557 33.333 0.00 0.00 32.46 3.06
1305 1322 1.883275 CCGCCAACATCAACAACCTTA 59.117 47.619 0.00 0.00 0.00 2.69
1383 1400 1.459348 TGGTGACTGGTCCAGCAGA 60.459 57.895 19.40 0.00 37.15 4.26
1416 1433 3.780173 GCCTCCTTCTGCCGAGCT 61.780 66.667 0.00 0.00 0.00 4.09
1485 1502 1.512926 AGCGGTCAAATGTGTCAGTC 58.487 50.000 0.00 0.00 0.00 3.51
1512 1529 0.694771 AAGAGCATCACCTTCCAGCA 59.305 50.000 0.00 0.00 37.82 4.41
1563 1580 9.593134 GGCATAAGATCAGTATATACAAAGAGG 57.407 37.037 15.18 0.00 0.00 3.69
1587 1604 0.827368 ACTAGCCTACTCAAGCTGGC 59.173 55.000 2.31 2.31 40.92 4.85
1615 1632 2.363683 CAGCAGGAAAGGATGAAGGTC 58.636 52.381 0.00 0.00 0.00 3.85
1698 1715 4.846779 TGTCAACTAAAACTGGATTGGC 57.153 40.909 0.00 0.00 0.00 4.52
1705 1723 8.352201 TCAGATGGATTTTGTCAACTAAAACTG 58.648 33.333 0.00 0.00 30.64 3.16
1706 1724 8.352942 GTCAGATGGATTTTGTCAACTAAAACT 58.647 33.333 0.00 0.00 30.64 2.66
1707 1725 7.595130 GGTCAGATGGATTTTGTCAACTAAAAC 59.405 37.037 0.00 0.00 30.64 2.43
1713 1731 3.670627 GCGGTCAGATGGATTTTGTCAAC 60.671 47.826 0.00 0.00 0.00 3.18
1830 1848 5.808042 AACAATTCTCGAATCATGGACAG 57.192 39.130 0.00 0.00 0.00 3.51
1848 1866 6.818644 GCAGAGTATCAGGACTTCAATAACAA 59.181 38.462 0.00 0.00 37.82 2.83
1930 1954 8.660435 AGCAGCTTAACATATAGGAAAGGATTA 58.340 33.333 0.00 0.00 0.00 1.75
1931 1955 7.446625 CAGCAGCTTAACATATAGGAAAGGATT 59.553 37.037 0.00 0.00 0.00 3.01
2161 2286 0.850100 ATGTTGGGTGAACTGGACCA 59.150 50.000 0.00 0.00 34.89 4.02
2182 2307 1.764851 CGAAGAAGCGAGATAGCCAG 58.235 55.000 0.00 0.00 38.01 4.85
2296 2421 1.000385 CGAACACCACGGTACCACTTA 60.000 52.381 13.54 0.00 0.00 2.24
2453 2578 8.620416 GCAACAACATACCAATGATAAGTGATA 58.380 33.333 0.00 0.00 36.54 2.15
2457 2582 6.625740 GCAGCAACAACATACCAATGATAAGT 60.626 38.462 0.00 0.00 36.54 2.24
2487 2613 1.229951 ATCCTCAGCCTTGGGACCA 60.230 57.895 0.00 0.00 31.48 4.02
2683 2809 1.801178 GAACTGCAAGCACTACAGGTC 59.199 52.381 3.67 3.67 40.63 3.85
2733 2859 6.128849 CCTTTGCATAAACAAGATTTTGACGG 60.129 38.462 2.48 0.00 37.73 4.79
2767 2893 4.026744 AGCCTCTACAATTCTGCTAGTGA 58.973 43.478 0.00 0.00 0.00 3.41
2772 2898 2.703007 CCCTAGCCTCTACAATTCTGCT 59.297 50.000 0.00 0.00 0.00 4.24
2775 2901 4.561752 ACATCCCTAGCCTCTACAATTCT 58.438 43.478 0.00 0.00 0.00 2.40
2843 2969 5.126061 ACCATGTTAGAGGATGCATTTTGAC 59.874 40.000 0.00 0.00 0.00 3.18
2873 3036 6.767902 AGAGCTCTTATTTATTTCGATGGCAA 59.232 34.615 11.45 0.00 0.00 4.52
2880 3043 6.980978 TGGTCTCAGAGCTCTTATTTATTTCG 59.019 38.462 15.27 0.00 0.00 3.46
2960 3128 7.861629 ACAGGATATATGAAAGACAACAAGGA 58.138 34.615 0.00 0.00 0.00 3.36
2999 3167 5.550011 TGGTAATGTGGGCATATGTAGGTAT 59.450 40.000 4.29 0.00 34.39 2.73
3049 3217 1.863454 CTGATGTAGCGACTTCATGCC 59.137 52.381 14.38 0.00 38.62 4.40
3054 3222 2.941453 TGGTCTGATGTAGCGACTTC 57.059 50.000 5.99 5.99 0.00 3.01
3055 3223 2.760650 TCATGGTCTGATGTAGCGACTT 59.239 45.455 0.00 0.00 0.00 3.01
3056 3224 2.360483 CTCATGGTCTGATGTAGCGACT 59.640 50.000 0.00 0.00 32.10 4.18
3057 3225 2.099921 ACTCATGGTCTGATGTAGCGAC 59.900 50.000 0.00 0.00 32.10 5.19
3058 3226 2.359214 GACTCATGGTCTGATGTAGCGA 59.641 50.000 6.98 0.00 41.46 4.93
3059 3227 2.099756 TGACTCATGGTCTGATGTAGCG 59.900 50.000 13.32 0.00 44.74 4.26
3061 3229 5.588958 TCTTGACTCATGGTCTGATGTAG 57.411 43.478 13.32 0.00 44.74 2.74
3062 3230 5.716703 TCTTCTTGACTCATGGTCTGATGTA 59.283 40.000 13.32 0.00 44.74 2.29
3064 3232 5.082251 TCTTCTTGACTCATGGTCTGATG 57.918 43.478 13.32 12.49 44.74 3.07
3065 3233 5.022122 TCTCTTCTTGACTCATGGTCTGAT 58.978 41.667 13.32 0.00 44.74 2.90
3066 3234 4.411013 TCTCTTCTTGACTCATGGTCTGA 58.589 43.478 13.32 9.63 44.74 3.27
3067 3235 4.797800 TCTCTTCTTGACTCATGGTCTG 57.202 45.455 13.32 8.02 44.74 3.51
3068 3236 5.022122 TGATCTCTTCTTGACTCATGGTCT 58.978 41.667 13.32 0.00 44.74 3.85
3069 3237 5.336150 TGATCTCTTCTTGACTCATGGTC 57.664 43.478 7.22 7.22 44.70 4.02
3070 3238 5.954153 ATGATCTCTTCTTGACTCATGGT 57.046 39.130 0.00 0.00 0.00 3.55
3106 3295 2.490903 ACTTCATGGCTTTCTGCATGAC 59.509 45.455 0.00 0.00 45.15 3.06
3233 3422 1.135972 GCATTGTTCGCGTTGTCTGAT 60.136 47.619 5.77 0.00 0.00 2.90
3433 3629 5.767168 GGCATAAGAAGCACCTCAATCTTAT 59.233 40.000 0.00 0.00 42.74 1.73
3602 3798 3.583806 ACGCTGAGAAGATGAAGAACAG 58.416 45.455 0.00 0.00 0.00 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.